Issues

• Keep test assertions live in Release builds

  matsengrp/larch2#45 · Filter by author matsen opened on Sep 17, 2026

• Add configurable checkpointing to the larch2 optimization loop

  matsengrp/larch2#39 · Filter by author matsen opened on Apr 27, 2026

• Treat IUPAC/gap positions as no-call in parsimony scoring

  matsengrp/larch2#36 · Filter by author matsen opened on Apr 19, 2026
  1

• Warn when input alignment contains IUPAC ambiguity codes

  matsengrp/larch2#35 · Filter by author matsen opened on Apr 18, 2026
  1

• larch2 sometimes fails to find the minimum parsimony score DAG

  matsengrp/larch2#33 · Filter by author matsen opened on Mar 30, 2026

• Add --dag-quick-info flag to dagutil

  matsengrp/larch2#25 · Filter by author matsen opened on Mar 26, 2026

• Add parsimony-bounded diverse tree sampling via quantile threshold

  matsengrp/larch2#12 · Filter by author matsen opened on Mar 18, 2026
  1

• Add greedy max-dispersion sampling (farthest-point-first over RF distance)

  matsengrp/larch2#5 · Filter by author matsen opened on Mar 18, 2026
  1

• Build & UX papercuts

  matsengrp/larch2#4 · Filter by author matsen opened on Mar 17, 2026